empty ABRicate results after conversion to FASTA format

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1

Hey there!
I converted FASTQ files to FASTA with the “FASTQ to FASTA” converter (on galaxy) as well as with the “any2fasta” tool I installed on my computer in order to run the “ABRicate” tool on it. But after the conversion ABRicate doesn’t give results. I’m sure that ABRicate should give results because when running MEGAHIT bfore running ABRIcate it also works. But the process is supposed to work without MEGAHIT. Do you have any idea, why the other conversion do not work?
Thanks in advance!

2

Hi @MelonaT,
could you share your Galaxy history with me? I’ll have a look at it. My email is Screenshot from 2022-04-03 16-52-09.

Regards

3

thanks, I shared it, the tests I were running basically start from job 112, where I uploaded a fasta file that I converted with any2fasta from fastq

4

Thanks @MelonaT,
I’m running a test; my feeling is that the problem is related to some not allowed characters present in the headers. I’ll let you know the result.

Regards

5

thank you so much!

6

Hi @MelonaT,
the problems is not related with the headers. It seems that ABRicate is not able to identify resistant genes when the raw reads are provided as input; it requires to assembly the reads into contigs (e.g. as you did with MEGAHIT) as previous step.

Regards

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